Starting phenix.real_space_refine on Sun Dec 10 22:33:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amw_15527/12_2023/8amw_15527.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amw_15527/12_2023/8amw_15527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amw_15527/12_2023/8amw_15527.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amw_15527/12_2023/8amw_15527.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amw_15527/12_2023/8amw_15527.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8amw_15527/12_2023/8amw_15527.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 104 5.16 5 C 10454 2.51 5 N 2553 2.21 5 O 2681 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15792 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 1965 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 254, 1956 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Conformer: "B" Number of residues, atoms: 254, 1956 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} bond proxies already assigned to first conformer: 2003 Chain: "B" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "C" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1956 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 11, 'TRANS': 242} Chain: "D" Number of atoms: 1974 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 1969 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} Conformer: "B" Number of residues, atoms: 256, 1969 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} bond proxies already assigned to first conformer: 2020 Chain: "E" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "F" Number of atoms: 1978 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 1969 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} Conformer: "B" Number of residues, atoms: 256, 1969 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 11, 'TRANS': 244} bond proxies already assigned to first conformer: 2016 Chain: "G" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "H" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1947 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 11, 'TRANS': 241} Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {'GOL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 30 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 4, 24 Unusual residues: {'GOL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Conformer: "B" Number of residues, atoms: 4, 24 Unusual residues: {'GOL': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} bond proxies already assigned to first conformer: 15 Chain: "D" Number of atoms: 12 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Conformer: "C" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 12 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 12 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 18 Unusual residues: {'GOL': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 12 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 6 Unusual residues: {'GOL': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AGLN A 145 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 145 " occ=0.50 residue: pdb=" N AALA D 23 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA D 23 " occ=0.50 residue: pdb=" N AGLN F 145 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN F 145 " occ=0.50 residue: pdb=" C1 AGOL C 402 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BGOL C 402 " occ=0.50 residue: pdb=" C1 AGOL D 401 " occ=0.38 ... (10 atoms not shown) pdb=" O3 CGOL D 401 " occ=0.62 residue: pdb=" C1 AGOL E 401 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BGOL E 401 " occ=0.50 residue: pdb=" C1 AGOL F 401 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BGOL F 401 " occ=0.50 residue: pdb=" C1 AGOL H 401 " occ=0.50 ... (10 atoms not shown) pdb=" O3 BGOL H 401 " occ=0.50 Time building chain proxies: 10.99, per 1000 atoms: 0.70 Number of scatterers: 15792 At special positions: 0 Unit cell: (93.104, 100.722, 121.035, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 104 16.00 O 2681 8.00 N 2553 7.00 C 10454 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.18 Conformation dependent library (CDL) restraints added in 3.9 seconds 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3574 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 0 sheets defined 78.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 27 through 30 Processing helix chain 'A' and resid 31 through 61 removed outlier: 3.561A pdb=" N PHE A 37 " --> pdb=" O MET A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 86 removed outlier: 3.806A pdb=" N VAL A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR A 79 " --> pdb=" O GLY A 75 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET A 80 " --> pdb=" O PHE A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 111 through 134 Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.640A pdb=" N PHE A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 190 Processing helix chain 'A' and resid 201 through 218 removed outlier: 3.939A pdb=" N VAL A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE A 206 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 241 Proline residue: A 232 - end of helix removed outlier: 3.536A pdb=" N GLY A 241 " --> pdb=" O THR A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 247 removed outlier: 3.712A pdb=" N VAL A 246 " --> pdb=" O GLY A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 254 No H-bonds generated for 'chain 'A' and resid 252 through 254' Processing helix chain 'A' and resid 255 through 276 Proline residue: A 261 - end of helix Processing helix chain 'B' and resid 27 through 30 Processing helix chain 'B' and resid 31 through 61 Processing helix chain 'B' and resid 66 through 86 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 111 through 134 Processing helix chain 'B' and resid 134 through 143 Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.560A pdb=" N ILE B 157 " --> pdb=" O THR B 154 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 158 " --> pdb=" O ALA B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 158' Processing helix chain 'B' and resid 167 through 190 removed outlier: 3.925A pdb=" N LEU B 173 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 218 removed outlier: 3.872A pdb=" N VAL B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 241 removed outlier: 3.566A pdb=" N ASP B 230 " --> pdb=" O ASN B 226 " (cutoff:3.500A) Proline residue: B 232 - end of helix removed outlier: 3.508A pdb=" N GLY B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 247 removed outlier: 3.958A pdb=" N VAL B 246 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 255 through 276 Proline residue: B 261 - end of helix Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 32 through 61 removed outlier: 3.562A pdb=" N PHE C 50 " --> pdb=" O VAL C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 86 removed outlier: 4.347A pdb=" N VAL C 78 " --> pdb=" O PHE C 74 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR C 79 " --> pdb=" O GLY C 75 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N MET C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 108 through 110 No H-bonds generated for 'chain 'C' and resid 108 through 110' Processing helix chain 'C' and resid 111 through 134 Processing helix chain 'C' and resid 134 through 143 Processing helix chain 'C' and resid 154 through 158 removed outlier: 3.572A pdb=" N PHE C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 190 removed outlier: 3.508A pdb=" N THR C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 218 removed outlier: 3.811A pdb=" N VAL C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 240 Proline residue: C 232 - end of helix Processing helix chain 'C' and resid 243 through 247 removed outlier: 3.747A pdb=" N VAL C 246 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 254 No H-bonds generated for 'chain 'C' and resid 252 through 254' Processing helix chain 'C' and resid 255 through 276 Proline residue: C 261 - end of helix Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 28 through 30 No H-bonds generated for 'chain 'D' and resid 28 through 30' Processing helix chain 'D' and resid 31 through 61 Processing helix chain 'D' and resid 66 through 90 removed outlier: 4.183A pdb=" N VAL D 78 " --> pdb=" O PHE D 74 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR D 79 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ARG D 87 " --> pdb=" O HIS D 83 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE D 88 " --> pdb=" O VAL D 84 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER D 89 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 134 removed outlier: 3.557A pdb=" N TYR D 115 " --> pdb=" O LYS D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 143 Processing helix chain 'D' and resid 154 through 158 removed outlier: 3.643A pdb=" N PHE D 158 " --> pdb=" O ALA D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 190 removed outlier: 3.513A pdb=" N GLY D 171 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 218 removed outlier: 3.889A pdb=" N VAL D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY D 218 " --> pdb=" O GLY D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 240 Proline residue: D 232 - end of helix Processing helix chain 'D' and resid 243 through 247 removed outlier: 3.941A pdb=" N VAL D 246 " --> pdb=" O GLY D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 254 No H-bonds generated for 'chain 'D' and resid 252 through 254' Processing helix chain 'D' and resid 255 through 276 Proline residue: D 261 - end of helix Processing helix chain 'E' and resid 31 through 61 removed outlier: 3.559A pdb=" N PHE E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 86 Processing helix chain 'E' and resid 94 through 104 Processing helix chain 'E' and resid 108 through 110 No H-bonds generated for 'chain 'E' and resid 108 through 110' Processing helix chain 'E' and resid 111 through 134 removed outlier: 3.523A pdb=" N TYR E 115 " --> pdb=" O LYS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 143 Processing helix chain 'E' and resid 154 through 158 removed outlier: 3.618A pdb=" N PHE E 158 " --> pdb=" O ALA E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 191 removed outlier: 3.509A pdb=" N THR E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 217 removed outlier: 3.736A pdb=" N VAL E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 240 removed outlier: 3.662A pdb=" N ASP E 230 " --> pdb=" O ASN E 226 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Proline residue: E 232 - end of helix Processing helix chain 'E' and resid 243 through 247 removed outlier: 3.991A pdb=" N VAL E 246 " --> pdb=" O GLY E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 254 No H-bonds generated for 'chain 'E' and resid 252 through 254' Processing helix chain 'E' and resid 255 through 276 Proline residue: E 261 - end of helix Processing helix chain 'F' and resid 24 through 30 Processing helix chain 'F' and resid 31 through 61 removed outlier: 3.796A pdb=" N ARG F 35 " --> pdb=" O ARG F 31 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU F 36 " --> pdb=" O LYS F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 86 removed outlier: 3.635A pdb=" N MET F 80 " --> pdb=" O PHE F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 104 Processing helix chain 'F' and resid 108 through 110 No H-bonds generated for 'chain 'F' and resid 108 through 110' Processing helix chain 'F' and resid 111 through 134 Processing helix chain 'F' and resid 134 through 143 Processing helix chain 'F' and resid 154 through 158 removed outlier: 3.555A pdb=" N ILE F 157 " --> pdb=" O THR F 154 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE F 158 " --> pdb=" O ALA F 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 154 through 158' Processing helix chain 'F' and resid 167 through 190 removed outlier: 3.511A pdb=" N THR F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 217 removed outlier: 3.875A pdb=" N VAL F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 241 Proline residue: F 232 - end of helix removed outlier: 3.578A pdb=" N GLY F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 249 removed outlier: 3.744A pdb=" N SER F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 254 No H-bonds generated for 'chain 'F' and resid 252 through 254' Processing helix chain 'F' and resid 255 through 276 Proline residue: F 261 - end of helix Processing helix chain 'G' and resid 26 through 30 Processing helix chain 'G' and resid 31 through 61 Processing helix chain 'G' and resid 66 through 86 Processing helix chain 'G' and resid 94 through 104 Processing helix chain 'G' and resid 108 through 110 No H-bonds generated for 'chain 'G' and resid 108 through 110' Processing helix chain 'G' and resid 111 through 134 Processing helix chain 'G' and resid 134 through 143 Processing helix chain 'G' and resid 154 through 158 removed outlier: 3.573A pdb=" N PHE G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 190 Processing helix chain 'G' and resid 201 through 218 removed outlier: 3.764A pdb=" N VAL G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY G 218 " --> pdb=" O GLY G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 240 Proline residue: G 232 - end of helix Processing helix chain 'G' and resid 244 through 249 removed outlier: 3.839A pdb=" N SER G 248 " --> pdb=" O LYS G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 254 No H-bonds generated for 'chain 'G' and resid 252 through 254' Processing helix chain 'G' and resid 255 through 276 Proline residue: G 261 - end of helix Processing helix chain 'H' and resid 26 through 30 Processing helix chain 'H' and resid 31 through 61 Processing helix chain 'H' and resid 66 through 86 removed outlier: 4.028A pdb=" N VAL H 78 " --> pdb=" O PHE H 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR H 79 " --> pdb=" O GLY H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 108 through 110 No H-bonds generated for 'chain 'H' and resid 108 through 110' Processing helix chain 'H' and resid 111 through 134 Processing helix chain 'H' and resid 134 through 143 Processing helix chain 'H' and resid 154 through 158 removed outlier: 3.602A pdb=" N ILE H 157 " --> pdb=" O THR H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 190 Processing helix chain 'H' and resid 201 through 218 removed outlier: 3.754A pdb=" N VAL H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY H 218 " --> pdb=" O GLY H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 241 Proline residue: H 232 - end of helix removed outlier: 3.591A pdb=" N GLY H 241 " --> pdb=" O THR H 237 " (cutoff:3.500A) Processing helix chain 'H' and resid 244 through 249 removed outlier: 3.741A pdb=" N SER H 248 " --> pdb=" O LYS H 244 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 254 No H-bonds generated for 'chain 'H' and resid 252 through 254' Processing helix chain 'H' and resid 255 through 276 Proline residue: H 261 - end of helix 1057 hydrogen bonds defined for protein. 3120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 6.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4763 1.34 - 1.46: 3124 1.46 - 1.57: 8146 1.57 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 16225 Sorted by residual: bond pdb=" C1 AGOL E 401 " pdb=" C2 AGOL E 401 " ideal model delta sigma weight residual 1.514 1.549 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" C2 GOL G 401 " pdb=" O2 GOL G 401 " ideal model delta sigma weight residual 1.410 1.378 0.032 2.00e-02 2.50e+03 2.60e+00 bond pdb=" C2 AGOL E 401 " pdb=" O2 AGOL E 401 " ideal model delta sigma weight residual 1.410 1.378 0.032 2.00e-02 2.50e+03 2.51e+00 bond pdb=" C2 BGOL H 401 " pdb=" O2 BGOL H 401 " ideal model delta sigma weight residual 1.410 1.378 0.032 2.00e-02 2.50e+03 2.51e+00 bond pdb=" C2 GOL B 401 " pdb=" O2 GOL B 401 " ideal model delta sigma weight residual 1.410 1.378 0.032 2.00e-02 2.50e+03 2.49e+00 ... (remaining 16220 not shown) Histogram of bond angle deviations from ideal: 98.56 - 105.66: 416 105.66 - 112.75: 8342 112.75 - 119.85: 5559 119.85 - 126.94: 7483 126.94 - 134.04: 265 Bond angle restraints: 22065 Sorted by residual: angle pdb=" N VAL H 258 " pdb=" CA VAL H 258 " pdb=" C VAL H 258 " ideal model delta sigma weight residual 112.96 109.54 3.42 1.00e+00 1.00e+00 1.17e+01 angle pdb=" CA TYR A 223 " pdb=" CB TYR A 223 " pdb=" CG TYR A 223 " ideal model delta sigma weight residual 113.90 118.69 -4.79 1.80e+00 3.09e-01 7.07e+00 angle pdb=" CA TYR D 223 " pdb=" CB TYR D 223 " pdb=" CG TYR D 223 " ideal model delta sigma weight residual 113.90 118.67 -4.77 1.80e+00 3.09e-01 7.02e+00 angle pdb=" CA TYR C 223 " pdb=" CB TYR C 223 " pdb=" CG TYR C 223 " ideal model delta sigma weight residual 113.90 118.66 -4.76 1.80e+00 3.09e-01 6.99e+00 angle pdb=" CA TYR G 223 " pdb=" CB TYR G 223 " pdb=" CG TYR G 223 " ideal model delta sigma weight residual 113.90 118.61 -4.71 1.80e+00 3.09e-01 6.85e+00 ... (remaining 22060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8573 17.89 - 35.78: 435 35.78 - 53.66: 81 53.66 - 71.55: 3 71.55 - 89.44: 4 Dihedral angle restraints: 9096 sinusoidal: 3412 harmonic: 5684 Sorted by residual: dihedral pdb=" CA PHE A 76 " pdb=" C PHE A 76 " pdb=" N GLY A 77 " pdb=" CA GLY A 77 " ideal model delta harmonic sigma weight residual 180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PHE F 76 " pdb=" C PHE F 76 " pdb=" N GLY F 77 " pdb=" CA GLY F 77 " ideal model delta harmonic sigma weight residual 180.00 159.86 20.14 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA PHE C 76 " pdb=" C PHE C 76 " pdb=" N GLY C 77 " pdb=" CA GLY C 77 " ideal model delta harmonic sigma weight residual 180.00 160.36 19.64 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 9093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1317 0.030 - 0.060: 805 0.060 - 0.090: 255 0.090 - 0.120: 62 0.120 - 0.150: 22 Chirality restraints: 2461 Sorted by residual: chirality pdb=" CA TYR C 223 " pdb=" N TYR C 223 " pdb=" C TYR C 223 " pdb=" CB TYR C 223 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA TYR A 223 " pdb=" N TYR A 223 " pdb=" C TYR A 223 " pdb=" CB TYR A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA TYR H 223 " pdb=" N TYR H 223 " pdb=" C TYR H 223 " pdb=" CB TYR H 223 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 2458 not shown) Planarity restraints: 2728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 226 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.96e+00 pdb=" N PRO E 227 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 227 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 227 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 162 " 0.027 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO D 163 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 163 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 163 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 231 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.58e+00 pdb=" N PRO G 232 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 232 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 232 " -0.022 5.00e-02 4.00e+02 ... (remaining 2725 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3421 2.78 - 3.31: 14371 3.31 - 3.84: 26054 3.84 - 4.37: 30116 4.37 - 4.90: 55260 Nonbonded interactions: 129222 Sorted by model distance: nonbonded pdb=" OD1 ASN C 101 " pdb=" O2 GOL C 403 " model vdw 2.245 2.440 nonbonded pdb=" OG SER F 142 " pdb=" O AGLN F 145 " model vdw 2.257 2.440 nonbonded pdb=" O3 GOL G 401 " pdb=" O1 GOL G 402 " model vdw 2.264 2.440 nonbonded pdb=" OG1 THR A 160 " pdb=" OD1 ASP A 230 " model vdw 2.279 2.440 nonbonded pdb=" O1 GOL C 401 " pdb=" O1 BGOL C 402 " model vdw 2.283 2.440 ... (remaining 129217 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'B' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'C' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'D' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'E' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'F' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'G' and (resid 25 through 144 or resid 146 through 277)) selection = (chain 'H' and (resid 25 through 144 or resid 146 through 277)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 13.860 Check model and map are aligned: 0.240 Set scattering table: 0.160 Process input model: 45.920 Find NCS groups from input model: 1.300 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16225 Z= 0.316 Angle : 0.610 5.978 22065 Z= 0.317 Chirality : 0.042 0.150 2461 Planarity : 0.005 0.050 2728 Dihedral : 11.059 89.440 5522 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.44 % Allowed : 5.56 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.19), residues: 2024 helix: 1.92 (0.14), residues: 1428 sheet: None (None), residues: 0 loop : -1.18 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 169 HIS 0.003 0.001 HIS G 57 PHE 0.012 0.002 PHE F 134 TYR 0.021 0.002 TYR C 223 ARG 0.002 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 1.719 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 193 average time/residue: 1.5415 time to fit residues: 324.8490 Evaluate side-chains 169 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 1.702 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.2198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 0.2980 chunk 181 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 140 HIS F 195 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16225 Z= 0.166 Angle : 0.520 5.995 22065 Z= 0.279 Chirality : 0.039 0.136 2461 Planarity : 0.005 0.048 2728 Dihedral : 4.825 40.520 2216 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.75 % Allowed : 10.62 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.19), residues: 2024 helix: 2.47 (0.14), residues: 1414 sheet: None (None), residues: 0 loop : -1.14 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 169 HIS 0.009 0.001 HIS F 140 PHE 0.010 0.001 PHE A 37 TYR 0.019 0.001 TYR C 223 ARG 0.003 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 1.591 Fit side-chains outliers start: 27 outliers final: 7 residues processed: 182 average time/residue: 1.4719 time to fit residues: 293.1433 Evaluate side-chains 168 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 161 time to evaluate : 1.624 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 1.0247 time to fit residues: 5.8701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 123 optimal weight: 0.3980 chunk 50 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 196 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.0862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16225 Z= 0.270 Angle : 0.565 6.178 22065 Z= 0.303 Chirality : 0.041 0.145 2461 Planarity : 0.005 0.047 2728 Dihedral : 4.979 43.511 2216 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.62 % Allowed : 12.81 % Favored : 85.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.19), residues: 2024 helix: 2.33 (0.14), residues: 1414 sheet: None (None), residues: 0 loop : -1.19 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 169 HIS 0.004 0.001 HIS G 57 PHE 0.011 0.002 PHE C 74 TYR 0.022 0.002 TYR C 223 ARG 0.006 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 1.733 Fit side-chains outliers start: 25 outliers final: 10 residues processed: 182 average time/residue: 1.5329 time to fit residues: 304.5083 Evaluate side-chains 175 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 1.471 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.8751 time to fit residues: 5.9863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.7980 chunk 136 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 193 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 ASN H 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16225 Z= 0.182 Angle : 0.517 6.134 22065 Z= 0.275 Chirality : 0.039 0.136 2461 Planarity : 0.005 0.047 2728 Dihedral : 4.760 41.486 2216 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.56 % Allowed : 14.00 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.20), residues: 2024 helix: 2.52 (0.14), residues: 1418 sheet: None (None), residues: 0 loop : -1.11 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 169 HIS 0.005 0.001 HIS D 57 PHE 0.012 0.001 PHE H 74 TYR 0.019 0.001 TYR C 223 ARG 0.005 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 1.660 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 182 average time/residue: 1.4397 time to fit residues: 287.3263 Evaluate side-chains 175 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 164 time to evaluate : 1.589 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.1472 time to fit residues: 2.4150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 164 optimal weight: 0.0000 chunk 133 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16225 Z= 0.236 Angle : 0.545 6.237 22065 Z= 0.290 Chirality : 0.040 0.144 2461 Planarity : 0.005 0.043 2728 Dihedral : 4.910 43.198 2216 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.81 % Allowed : 14.19 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.19), residues: 2024 helix: 2.50 (0.14), residues: 1398 sheet: None (None), residues: 0 loop : -1.28 (0.26), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 169 HIS 0.005 0.001 HIS F 57 PHE 0.022 0.001 PHE A 74 TYR 0.021 0.002 TYR C 223 ARG 0.003 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 164 time to evaluate : 1.802 Fit side-chains outliers start: 28 outliers final: 12 residues processed: 184 average time/residue: 1.5077 time to fit residues: 303.6586 Evaluate side-chains 174 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 162 time to evaluate : 1.720 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 2.4735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 113 optimal weight: 0.3980 chunk 47 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16225 Z= 0.166 Angle : 0.501 6.302 22065 Z= 0.267 Chirality : 0.038 0.134 2461 Planarity : 0.004 0.044 2728 Dihedral : 4.619 39.583 2216 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.75 % Allowed : 14.62 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.20), residues: 2024 helix: 2.60 (0.14), residues: 1428 sheet: None (None), residues: 0 loop : -1.29 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 169 HIS 0.005 0.001 HIS D 57 PHE 0.010 0.001 PHE A 37 TYR 0.018 0.001 TYR C 223 ARG 0.003 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.664 Fit side-chains outliers start: 27 outliers final: 13 residues processed: 187 average time/residue: 1.4670 time to fit residues: 300.4127 Evaluate side-chains 179 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 166 time to evaluate : 1.724 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 0 time to fit residues: 2.2381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.4980 chunk 21 optimal weight: 0.0040 chunk 110 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 192 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 117 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 16225 Z= 0.153 Angle : 0.493 6.596 22065 Z= 0.260 Chirality : 0.037 0.129 2461 Planarity : 0.004 0.041 2728 Dihedral : 4.447 50.727 2216 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.56 % Allowed : 15.25 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.20), residues: 2024 helix: 2.83 (0.14), residues: 1408 sheet: None (None), residues: 0 loop : -1.38 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 169 HIS 0.005 0.001 HIS D 57 PHE 0.016 0.001 PHE A 74 TYR 0.017 0.001 TYR D 223 ARG 0.003 0.000 ARG F 87 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 169 time to evaluate : 1.681 Fit side-chains outliers start: 24 outliers final: 14 residues processed: 188 average time/residue: 1.4906 time to fit residues: 308.3315 Evaluate side-chains 180 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 166 time to evaluate : 1.770 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 1.2659 time to fit residues: 5.0273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 0.0270 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 151 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16225 Z= 0.162 Angle : 0.501 7.834 22065 Z= 0.263 Chirality : 0.038 0.132 2461 Planarity : 0.004 0.041 2728 Dihedral : 4.343 44.295 2216 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.31 % Allowed : 15.62 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.20), residues: 2024 helix: 2.83 (0.14), residues: 1408 sheet: None (None), residues: 0 loop : -1.36 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 169 HIS 0.005 0.001 HIS D 57 PHE 0.010 0.001 PHE A 37 TYR 0.017 0.001 TYR D 223 ARG 0.007 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.510 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 184 average time/residue: 1.4597 time to fit residues: 294.2407 Evaluate side-chains 181 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 1.750 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 2.3896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 3.9990 chunk 168 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 169 optimal weight: 0.9990 chunk 117 optimal weight: 0.0970 chunk 189 optimal weight: 5.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16225 Z= 0.161 Angle : 0.501 10.688 22065 Z= 0.263 Chirality : 0.038 0.128 2461 Planarity : 0.004 0.041 2728 Dihedral : 4.415 55.079 2216 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.38 % Allowed : 15.75 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.20), residues: 2024 helix: 2.85 (0.14), residues: 1408 sheet: None (None), residues: 0 loop : -1.35 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 169 HIS 0.005 0.001 HIS E 140 PHE 0.020 0.001 PHE A 74 TYR 0.019 0.001 TYR C 223 ARG 0.008 0.000 ARG D 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 1.585 Fit side-chains outliers start: 21 outliers final: 13 residues processed: 186 average time/residue: 1.4568 time to fit residues: 296.7753 Evaluate side-chains 177 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 164 time to evaluate : 1.593 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.1319 time to fit residues: 2.4257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 132 optimal weight: 0.4980 chunk 199 optimal weight: 4.9990 chunk 183 optimal weight: 0.0370 chunk 158 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 126 optimal weight: 0.0370 chunk 169 optimal weight: 4.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 16225 Z= 0.150 Angle : 0.494 11.321 22065 Z= 0.257 Chirality : 0.037 0.129 2461 Planarity : 0.004 0.041 2728 Dihedral : 4.215 50.376 2216 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.25 % Allowed : 15.88 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.20), residues: 2024 helix: 2.92 (0.14), residues: 1412 sheet: None (None), residues: 0 loop : -1.29 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 169 HIS 0.005 0.001 HIS D 57 PHE 0.009 0.001 PHE A 37 TYR 0.016 0.001 TYR D 223 ARG 0.009 0.000 ARG D 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4048 Ramachandran restraints generated. 2024 Oldfield, 0 Emsley, 2024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 173 time to evaluate : 1.698 Fit side-chains outliers start: 19 outliers final: 12 residues processed: 191 average time/residue: 1.4269 time to fit residues: 300.0519 Evaluate side-chains 187 residues out of total 1596 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 175 time to evaluate : 1.501 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 2.0461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 1.9990 chunk 146 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 163 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 57 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.127343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.102904 restraints weight = 38443.538| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 2.51 r_work: 0.3021 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16225 Z= 0.183 Angle : 0.520 11.290 22065 Z= 0.272 Chirality : 0.038 0.132 2461 Planarity : 0.005 0.040 2728 Dihedral : 4.454 55.040 2216 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.06 % Allowed : 16.38 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.20), residues: 2024 helix: 2.81 (0.14), residues: 1408 sheet: None (None), residues: 0 loop : -1.33 (0.26), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 169 HIS 0.005 0.001 HIS H 57 PHE 0.023 0.001 PHE A 74 TYR 0.018 0.001 TYR D 223 ARG 0.008 0.000 ARG D 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5170.62 seconds wall clock time: 92 minutes 43.34 seconds (5563.34 seconds total)